Merge branch 'master' into staging

1 files changed, 212 insertions, 29 deletions

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bc5ff3d2d8..2428608a30 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -671,6 +671,26 @@ API for locking files.")
 (define-public python2-lockfile
   (package-with-python2 python-lockfile))
 
+(define-public python-filelock
+  (package
+    (name "python-filelock")
+    (version "3.0.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "filelock" version))
+       (sha256
+        (base32
+         "0ngzlvb5j8gqs2nxlp2b0jhzii792h66wsn694qm8kqixr225n0q"))))
+    (build-system python-build-system)
+    (home-page
+     "https://github.com/benediktschmitt/py-filelock")
+    (synopsis "Platform independent file lock")
+    (description "@code{filelock} contains a single module implementing
+a platform independent file lock in Python, which provides a simple way of
+inter-process communication.")
+    (license license:unlicense)))
+
 (define-public python-semantic-version
   (package
     (name "python-semantic-version")
@@ -2378,28 +2398,30 @@ e.g. filters, callbacks and errbacks can all be promises.")
 (define-public python-virtualenv
   (package
     (name "python-virtualenv")
-    (version "16.1.0")
+    (version "20.0.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "virtualenv" version))
        (sha256
         (base32
-         "0242cg3hdq3qdvx5flyrki8lpwlgwf5k45c21ks5049fv7ygm6gq"))))
+         "096r7g5cv85vxymg9iqbn5z749613snlvd6p3rf1nxnrd386j0qz"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'disable-failing-test
-           (lambda _
-             ;; Disable failing test.  See upstream bug report
-             ;; https://github.com/pypa/virtualenv/issues/957
-             (substitute* "tests/test_virtualenv.py"
-               (("skipif.*") "skipif(True, reason=\"Guix\")\n"))
-             #t)))))
     (native-inputs
      `(("python-mock" ,python-mock)
-       ("python-pytest" ,python-pytest)))
+       ("python-pytest" ,python-pytest)
+       ;; NOTE: guix lint remarks that "python-setuptools should probably not
+       ;; be an input at all". However, removing the input makes the build error:
+       ;; File "setup.py", line 4, in <module>
+       ;;   raise RuntimeError("setuptools >= 41 required to build")
+       ("python-setuptools" ,python-setuptools)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
+    (inputs
+     `(("python-appdirs" ,python-appdirs)
+       ("python-distlib" ,python-distlib)
+       ("python-filelock" ,python-filelock)
+       ("python-six" ,python-six)
+       ("python-importlib-metadata" ,python-importlib-metadata)))
     (home-page "https://virtualenv.pypa.io/")
     (synopsis "Virtual Python environment builder")
     (description
@@ -3175,17 +3197,36 @@ used in text editing environments to provide a complete and integrated
 feature-set for programming Python effectively.")
     (license license:expat)))
 
+(define-public python-pathspec
+  (package
+    (name "python-pathspec")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pathspec" version))
+       (sha256
+        (base32
+         "15lvs4awlg8xzl0l4gk9y53xx4yqmqvsv44pglv39m70y85afajn"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/cpburnz/python-path-specification")
+    (synopsis "Utility library for gitignore style pattern matching of file paths")
+    (description
+     "This package provides a utility library for gitignore style pattern
+matching of file paths.")
+    (license license:mpl2.0)))
+
 (define-public python-black
   (package
     (name "python-black")
-    (version "18.6b4")
+    (version "19.10b0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "black" version))
        (sha256
         (base32
-         "0i4sfqgz6w15vd50kbhi7g7rifgqlf8yfr8y78rypd56q64qn592"))))
+         "0f8mr0yzj78q1dx7v6ggbgfir2wv0n5z2shfbbvfdq7910xbgvf2"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -3195,16 +3236,39 @@ feature-set for programming Python effectively.")
              (let ((python3 (which "python3")))
                (substitute* '("tests/data/fmtonoff.py"
                               "tests/data/string_prefixes.py"
-                              "tests/data/function.py")
+                              "tests/data/function.py"
+                              "tests/data/python37.py")
                  (("#!/usr/bin/env python3(\\.[0-9]+)?" _ minor-version)
                   (string-append "#!" python3 (if (string? minor-version)
                                                   minor-version
-                                                  ""))))))))))
+                                                  "")))))
+             #t))
+         (add-after 'unpack 'disable-broken-tests
+           (lambda _
+             ;; These tests are supposed to be skipped when the blackd
+             ;; dependencies are missing, but this doesn't quite work.
+             (substitute* "tests/test_black.py"
+               (("( *)class BlackDTestCase.*" match indent)
+                (string-append indent "@unittest.skip(\"no blackd deps\")\n"
+                               indent "class BlackDTestCase(unittest.TestCase):\n"))
+               (("web.Application") "False")
+               (("@unittest_run_loop") ""))
+
+             ;; Patching the above file breaks the self test
+             (substitute* "tests/test_black.py"
+               (("( *)def test_self" match indent)
+                (string-append indent "@unittest.skip(\"guix\")\n" match)))
+             #t)))))
     (propagated-inputs
      `(("python-click" ,python-click)
        ("python-attrs" ,python-attrs)
        ("python-appdirs" ,python-appdirs)
-       ("python-toml" ,python-toml)))
+       ("python-pathspec" ,python-pathspec)
+       ("python-regex" ,python-regex)
+       ("python-toml" ,python-toml)
+       ("python-typed-ast" ,python-typed-ast)))
+    (native-inputs
+     `(("python-setuptools-scm" ,python-setuptools-scm)))
     (home-page "https://github.com/ambv/black")
     (synopsis "The uncompromising code formatter")
     (description "Black is the uncompromising Python code formatter.")
@@ -3743,21 +3807,20 @@ color scales, and color space conversion easy.  It has support for:
 (define-public python-pygit2
   (package
     (name "python-pygit2")
-    (version "0.28.2")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pygit2" version))
        (sha256
-        (base32 "11kzj5mjkspvplnpdb6bj8dcj6rgmkk986k8hjcklyg5yaxkz32d"))))
+        (base32 "1hs0pqqzn1yjxqk86nq7p0lvsklwnlyi5xwyzr7d5nrs19dmsjbg"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f))            ; tests don't run correctly in our environment
     (propagated-inputs
-     `(("python-six" ,python-six)
+     `(("python-cached-property" ,python-cached-property)
        ("python-cffi" ,python-cffi)
-       ("libgit2" ,libgit2)
-       ("python-tox" ,python-tox)))
+       ("libgit2" ,libgit2)))
     (native-inputs
      `(("python-pytest" ,python-pytest)))
     (home-page "https://github.com/libgit2/pygit2")
@@ -3767,9 +3830,6 @@ library, libgit2 implements Git plumbing.")
     ;; GPL2.0 only, with linking exception.
     (license license:gpl2)))
 
-(define-public python2-pygit2
-  (package-with-python2 python-pygit2))
-
 (define-public python-pyparsing
   (package
     (name "python-pyparsing")
@@ -4413,6 +4473,40 @@ by pycodestyle.")
 (define-public python2-autopep8
   (package-with-python2 python-autopep8))
 
+(define-public python-distlib
+  (package
+    (name "python-distlib")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "distlib" version ".zip"))
+       (sha256
+        (base32
+         "08fyi2r246733vharl2yckw20rilci28r91mzrnnvcr638inw5if"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'no-/bin/sh
+           (lambda _
+             (substitute* '("distlib/scripts.py" "tests/test_scripts.py")
+               (("/bin/sh") (which "sh")))
+             #t))
+         (add-before 'check 'prepare-test-env
+           (lambda _
+             (setenv "HOME" "/tmp")
+             ;; NOTE: Any value works, the variable just has to be present.
+             (setenv "SKIP_ONLINE" "1")
+             #t)))))
+    (native-inputs `(("unzip" ,unzip)))
+    (home-page "https://bitbucket.org/pypa/distlib")
+    (synopsis "Distribution utilities")
+    (description "Distlib is a library which implements low-level functions that
+relate to packaging and distribution of Python software.  It is intended to be
+used as the basis for third-party packaging tools.")
+    (license license:psfl)))
+
 (define-public python-distutils-extra
   (package
     (name "python-distutils-extra")
@@ -7236,6 +7330,12 @@ printing of sub-tables by specifying a row range.")
                                "linker_exe='gcc',"
                                "linker_so='gcc -shared')")))
              #t))
+         (add-after 'unpack 'disable-tuning
+           (lambda _
+             (substitute* "setup.py"
+               (("cpu_flags = .*")
+                "cpu_flags = ['sse2']\n"))
+             #t))
          (replace 'build
            (lambda* (#:key inputs #:allow-other-keys)
              (invoke "python" "setup.py" "build"
@@ -7253,7 +7353,7 @@ printing of sub-tables by specifying a row range.")
      `(("python-cython" ,python-cython)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("hdf5" ,hdf5)
+     `(("hdf5" ,hdf5-1.10)
        ("bzip2" ,bzip2)
        ("zlib" ,zlib)))
     (home-page "http://www.pytables.org/")
@@ -7265,6 +7365,84 @@ designed to efficiently cope with extremely large amounts of data.")
 (define-public python2-tables
   (package-with-python2 python-tables))
 
+(define-public python-pytest-black
+  (package
+    (name "python-pytest-black")
+    (version "0.3.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-black" version))
+       (sha256
+        (base32
+         "04lppqydxm0f3f3x0l8hj7v0j6d8syj34jc37yzqwqcyqsnaga81"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-black" ,python-black)
+       ("python-toml" ,python-toml)))
+    (native-inputs
+     `(("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://github.com/shopkeep/pytest-black")
+    (synopsis "Pytest plugin to enable format checking with black")
+    (description
+     "This package provides a pytest plugin to enable format checking with the
+Python code formatter \"black\".")
+    (license license:expat)))
+
+(define-public python-get-version
+  (package
+    (name "python-get-version")
+    (version "2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "get_version" version))
+       (sha256
+        (base32
+         "1g15jyx33vkxavv9hwv275cs4g9bp2i1y942raw3fxamq8kbaml1"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pygments" ,python-pygments)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-black" ,python-pytest-black)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-setuptools" ,python-setuptools)
+       ("python-testpath" ,python-testpath)))
+    (home-page "https://github.com/flying-sheep/get_version")
+    (synopsis "Version helper in the spirit of versioneer")
+    (description
+     "This package provides a version helper that lets you automatically use
+the latest @code{vX.X.X} Git tag as the version in your Python package.  It
+also supports getting the version from Python source distributions or, once
+your package is installed, via @code{pkg_resources} (part of
+@code{setuptools}).")
+    (license license:gpl3+)))
+
+(define-public python-legacy-api-wrap
+  (package
+    (name "python-legacy-api-wrap")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "legacy-api-wrap" version))
+       (sha256
+        (base32
+         "06qhp0g543dy98vpa41hwdalvdbsjfc3ldk474yr9sd75mhl8jh3"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-get-version" ,python-get-version)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-black" ,python-pytest-black)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "https://github.com/flying-sheep/legacy-api-wrap")
+    (synopsis "Legacy API wrapper")
+    (description "This module defines a decorator to wrap legacy APIs.  The
+primary use case is APIs defined before keyword-only parameters existed.")
+    (license license:gpl3+)))
+
 (define-public python-pyasn1
   (package
     (name "python-pyasn1")
@@ -8479,7 +8657,7 @@ minimal and fast API targeting the following uses:
 @item write and deploy hybrid multi-process applications
 @item write scripts to administer multiple environments
 @end enumerate")
-    (home-page "http://codespeak.net/execnet/")
+    (home-page "https://codespeak.net/execnet/")
     (license license:expat)))
 
 (define-public python2-execnet
@@ -14421,7 +14599,12 @@ such as figshare or Zenodo.")
          "183kg1rhzz3hqizvphkd8hlbf1zxfx8737zhfkmqzxi71jmdw7pd"))))
     (build-system python-build-system)
     (native-inputs
-     `(("python-tox" ,python-tox)
+     `(("python-appdirs" ,python-appdirs)
+       ("python-distlib" ,python-distlib)
+       ("python-importlib-metadata" ,python-importlib-metadata)
+       ("python-filelock" ,python-filelock)
+       ("python-six" ,python-six)
+       ("python-tox" ,python-tox)
        ("python-virtualenv" ,python-virtualenv)))
     (home-page "https://github.com/k-bx/python-semver")
     (synopsis "Python helper for Semantic Versioning")